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install only from BiocManager, update vignette #13

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2 changes: 1 addition & 1 deletion .github/workflows/basic_checks.yaml
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Expand Up @@ -34,7 +34,7 @@ jobs:
run: |
options(repos = c(CRAN = "https://cran.r-project.org"))
BiocManager::repositories()
remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install("seandavi/BuildABiocWorkshop2020", dependencies = TRUE, update = TRUE, ask = FALSE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -4,4 +4,4 @@ WORKDIR /home/rstudio

COPY --chown=rstudio:rstudio . /home/rstudio/

RUN Rscript -e "devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"
RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install('seandavi/BuildABiocWorkshop2020', dependencies=TRUE, build_vignettes=TRUE, update = TRUE, ask = FALSE)"
28 changes: 28 additions & 0 deletions vignettes/HOWTO_BUILD_WORKSHOP.Rmd
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Expand Up @@ -50,6 +50,10 @@ desired Docker image name**. In other words, this section of the
github actions file will build and push to dockerhub the image with
this name.

**NOTE**: Dockerhub names must be all lowercase, can be two to 255
characters, and can only contain lowercase letters, numbers or `-` and
`_` (https://docs.docker.com/docker-hub/repos/).


```yaml
- uses: docker/build-push-action@v1
Expand All @@ -64,6 +68,30 @@ this name.
tags: latest
```

Also change the repo name here (here it is case-insensitive):

```yaml
- name: Install dependencies
run: |
options(repos = c(CRAN = "https://cran.r-project.org"))
BiocManager::repositories()
BiocManager::install("seandavi/BuildABiocWorkshop2020", dependencies = TRUE, update = TRUE, ask = FALSE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
```

### Edit `Dockerfile`

Change `seandavi/BuildABiocWorkshop2020` to the username/reponame of
your GitHub repo, to install your workshop and all its
Depends/Imports/Suggests and their dependencies into the Docker
container for your workshop.

You can also choose to build on a different base Bioconductor Docker
image. For example, to build on release 3.11 instead of devel, change
`FROM bioconductor/bioconductor_docker:devel` to `FROM
bioconductor/bioconductor_docker:RELEASE_3_11`.

### Add "secrets" to github repo

Secrets are encrypted environment variables that you create in a
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